LAMMPS (27 Nov 2018)
  using 1 OpenMP thread(s) per MPI task
# 2d rounded polygon bodies

variable    r     index 4
variable    steps index 100000
variable    T     index 0.5
variable    P     index 0.1
variable    seed  index 980411

units       lj
dimension   2

atom_style  body rounded/polygon 1 6
atom_modify map array
read_data   data.squares
  orthogonal box = (0 0 -0.5) to (12 12 0.5)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  2 atoms
  2 bodies

replicate   $r $r 1
replicate   4 $r 1
replicate   4 4 1
  orthogonal box = (0 0 -0.5) to (48 48 0.5)
  1 by 1 by 1 MPI processor grid
  32 atoms
  Time spent = 0.000279665 secs

velocity    all create $T ${seed} dist gaussian mom yes rot yes
velocity    all create 0.5 ${seed} dist gaussian mom yes rot yes
velocity    all create 0.5 980411 dist gaussian mom yes rot yes

variable cut_inner  equal 0.5
variable k_n        equal 100
variable k_na       equal 2
variable c_n        equal 1
variable c_t        equal 1
variable mu         equal 0.1
variable delta_ua   equal 0.5

pair_style body/rounded/polygon ${c_n} ${c_t} ${mu} ${delta_ua} ${cut_inner}
pair_style body/rounded/polygon 1 ${c_t} ${mu} ${delta_ua} ${cut_inner}
pair_style body/rounded/polygon 1 1 ${mu} ${delta_ua} ${cut_inner}
pair_style body/rounded/polygon 1 1 0.1 ${delta_ua} ${cut_inner}
pair_style body/rounded/polygon 1 1 0.1 0.5 ${cut_inner}
pair_style body/rounded/polygon 1 1 0.1 0.5 0.5
pair_coeff * * ${k_n} ${k_na}
pair_coeff * * 100 ${k_na}
pair_coeff * * 100 2

comm_modify vel yes

neighbor     0.5 bin
neigh_modify every 1 delay 0 check yes

timestep     0.001

#fix         1 all nve/body
#fix         1 all nvt/body temp $T $T 1.0
fix          1 all npt/body temp $T $T 1.0 x 0.001 $P 1.0              y 0.001 $P 1.0 couple xy fixedpoint 0 0 0
fix          1 all npt/body temp 0.5 $T 1.0 x 0.001 $P 1.0              y 0.001 $P 1.0 couple xy fixedpoint 0 0 0
fix          1 all npt/body temp 0.5 0.5 1.0 x 0.001 $P 1.0              y 0.001 $P 1.0 couple xy fixedpoint 0 0 0
fix          1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0              y 0.001 $P 1.0 couple xy fixedpoint 0 0 0
fix          1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0              y 0.001 0.1 1.0 couple xy fixedpoint 0 0 0

fix          2 all enforce2d

#compute      1 all body/local id 1 2 3
#dump         1 all local 100000 dump.polygon.* index c_1[1] c_1[2] c_1[3] c_1[4]

thermo_style custom step ke pe etotal press
thermo       1000

#dump	     2 all image 10000 image.*.jpg type type zoom 2.0 #             adiam 1.5 body type 0 0
#dump_modify  2 pad 6

run          ${steps}
run          100000
Neighbor list info ...
  update every 1 steps, delay 0 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 6.15685
  ghost atom cutoff = 6.15685
  binsize = 3.07843, bins = 16 16 1
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair body/rounded/polygon, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton
      stencil: half/bin/2d/newton
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.781 | 4.781 | 4.781 Mbytes
Step KinEng PotEng TotEng Press 
       0     0.484375         0.25     0.734375 0.0067274306 
    1000   0.38428256 0.0014168922   0.38569945 0.0020468171 
    2000   0.41372193  0.015263236   0.42898517 0.0029343462 
    3000   0.54844547  0.014870378   0.56331585  0.001978353 
    4000   0.73816048  0.031668204   0.76982869 0.0025939718 
    5000   0.84536165  0.011504649    0.8568663 0.0037990517 
    6000   0.73776478   0.14445932    0.8822241 0.0086538113 
    7000   0.52022565  0.069507637   0.58973329 0.0072098694 
    8000   0.72653213   0.12783368   0.85436581  0.023907183 
    9000   0.87685727    0.1239819    1.0008392 0.0064590959 
   10000    0.7250918  0.097243508   0.82233531 0.0012448267 
   11000   0.62302234   0.05597557   0.67899791 0.00080239872 
   12000   0.57159363   0.18199602   0.75358965   0.01033626 
   13000    0.7505295  0.071545266   0.82207477  0.011480236 
   14000   0.84703598   0.15914379    1.0061798  0.032814039 
   15000   0.41905013  0.090552572    0.5096027  0.015717153 
   16000   0.41805189  0.042916881   0.46096877  0.020702707 
   17000   0.59966233   0.05285043   0.65251275  0.016526024 
   18000   0.54282285   0.20835047   0.75117332  0.036414059 
   19000     0.777922  0.034754101    0.8126761  0.036467537 
   20000   0.54703924   0.14633506    0.6933743  0.012917248 
   21000   0.49337931    0.1858754   0.67925471  0.037890735 
   22000   0.64916623   0.19281344   0.84197967  0.011996773 
   23000   0.66958738   0.20459682    0.8741842  0.023639466 
   24000   0.63729755    0.1111959   0.74849345  0.025049919 
   25000   0.60094316   0.13375799   0.73470115  0.035286376 
   26000   0.35419589   0.22049451    0.5746904 0.0024215291 
   27000   0.33789786   0.18494942   0.52284728 0.0066457643 
   28000   0.32376056   0.13151726   0.45527782  0.010773856 
   29000   0.36198203   0.11044834   0.47243037  0.063012638 
   30000   0.22624436   0.19690087   0.42314523  0.037422734 
   31000   0.32284312  0.059623656   0.38246677    0.0287682 
   32000    0.4457193  0.042396136   0.48811544  0.022025252 
   33000   0.61078662  0.059447221   0.67023384  0.030335089 
   34000   0.63157762  0.062056279    0.6936339  0.044624352 
   35000   0.69577644  0.086216204   0.78199264    0.0319995 
   36000   0.76814336  0.062105963   0.83024933  0.044316891 
   37000   0.58641664  0.095034548   0.68145119   0.03234133 
   38000   0.48772813   0.12911854   0.61684667  0.038732146 
   39000   0.74957742   0.09823432   0.84781174  0.053181162 
   40000   0.57881374    0.2932491   0.87206284  0.065740126 
   41000    0.4415176   0.22899179   0.67050939  0.026159841 
   42000    0.5260339    0.2048105    0.7308444  0.046294432 
   43000   0.33493572   0.32500572   0.65994144  -0.01250241 
   44000   0.46467243   0.07907132   0.54374375   0.13386238 
   45000   0.48135518    0.2618908   0.74324598 -0.016767159 
   46000   0.27223209   0.24562643   0.51785852  0.052118439 
   47000   0.26402739    0.1838767   0.44790409 -0.0015878764 
   48000   0.10229166   0.25519169   0.35748335 -0.033927088 
   49000   0.24313495   0.16578185   0.40891679   0.12414926 
   50000   0.27400066   0.27688032   0.55088098   0.10421157 
   51000   0.43081855   0.18111733   0.61193587   0.16373371 
   52000   0.81969298  0.060995894   0.88068887  0.057285357 
   53000   0.99936159  0.029137886    1.0284995   0.19425015 
   54000   0.69750047  0.038079774   0.73558024 -0.089236384 
   55000   0.54823746  0.056369886   0.60460734 -0.021320579 
   56000    0.6752322  0.050322917   0.72555512   0.25303548 
   57000   0.90328009  0.061107142   0.96438723   -0.1962713 
   58000   0.81463148  0.050387847   0.86501933   0.35952157 
   59000   0.61636455  0.064910223   0.68127478  -0.27208497 
   60000   0.62573918  0.052264617   0.67800379    0.4493407 
   61000   0.81065726  0.071269668   0.88192693  -0.34643283 
   62000   0.86420318  0.052799365   0.91700254   0.48308047 
   63000   0.67848508  0.069087342   0.74757242  -0.31814526 
   64000   0.61430417  0.052109373   0.66641354   0.38336646 
   65000   0.75782937  0.063488206   0.82131757  -0.19113322 
   66000   0.88735857  0.051779306   0.93913787   0.29410996 
   67000   0.70684373  0.061786313   0.76863005  -0.16503578 
   68000   0.58571951  0.052402151   0.63812166   0.30173228 
   69000   0.64997491  0.064435462   0.71441037   -0.1920633 
   70000   0.75071821  0.053416991    0.8041352    0.3846747 
   71000    0.8124718   0.06877986   0.88125166  -0.26852566 
   72000   0.71352066   0.05358784    0.7671085   0.41321806 
   73000   0.55151827  0.066470642   0.61798891   -0.2211738 
   74000   0.65473635  0.061946814   0.71668316   0.29536873 
   75000   0.88704613  0.059476353   0.94652248   -0.0312656 
   76000   0.76899803  0.057351665    0.8263497  0.017885214 
   77000   0.65149455   0.05407174   0.70556629   0.25192449 
   78000   0.68614394  0.074251169   0.76039511  -0.19369404 
   79000   0.97451567   0.06262739    1.0371431    0.4217182 
   80000   0.88207775  0.070157004   0.95223476  -0.27318477 
   81000   0.69294455  0.062623957   0.75556851   0.40150141 
   82000   0.70748016  0.073924331   0.78140449  -0.17128794 
   83000   0.78180774  0.063513978   0.84532172   0.22033652 
   84000   0.80170993  0.065812223   0.86752216  0.083202913 
   85000   0.64788122  0.070348079    0.7182293 -0.066913668 
   86000   0.56575431  0.064865112   0.63061942   0.33905786 
   87000   0.78205358   0.07983702    0.8618906  -0.22844912 
   88000   0.87426443  0.065703482   0.93996791     0.448573 
   89000   0.73269893  0.079827385   0.81252632  -0.24183162 
   90000   0.66703106  0.065630146   0.73266121   0.35410109 
   91000   0.73107154   0.07402702   0.80509856 -0.085492997 
   92000     1.043635  0.067156523    1.1107915   0.14311135 
   93000   0.86063344  0.065607238   0.92624068   0.20750649 
   94000   0.68304235  0.075962239   0.75900459  -0.14594625 
   95000    0.7069191  0.067125732   0.77404483   0.39459759 
   96000   0.79860046  0.090957588   0.88955805  -0.24202125 
   97000   0.81366777  0.071387081   0.88505485   0.32217266 
   98000   0.61885746  0.041524228   0.66038169   0.31635364 
   99000   0.57007759  0.055438456   0.62551604  -0.21172902 
  100000   0.80462394  0.045542313   0.85016626  0.099207503 
Loop time of 6.34495 on 1 procs for 100000 steps with 32 atoms

Performance: 1361713.788 tau/day, 15760.576 timesteps/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 5.0158     | 5.0158     | 5.0158     |   0.0 | 79.05
Neigh   | 0.0072868  | 0.0072868  | 0.0072868  |   0.0 |  0.11
Comm    | 0.18669    | 0.18669    | 0.18669    |   0.0 |  2.94
Output  | 0.00098681 | 0.00098681 | 0.00098681 |   0.0 |  0.02
Modify  | 1.0417     | 1.0417     | 1.0417     |   0.0 | 16.42
Other   |            | 0.09245    |            |       |  1.46

Nlocal:    32 ave 32 max 32 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    35 ave 35 max 35 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    61 ave 61 max 61 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 61
Ave neighs/atom = 1.90625
Neighbor list builds = 1545
Dangerous builds = 0
Total wall time: 0:00:06
